Goes to show that not all ls990s are created equal. I had issues UNTIL I wiped internal(no micro SD currently). I didn't use flashtool though. I wiped everything in twrp then sideloaded barepopv2. No issues. Before that I had some of the same issues you had but only wiped dalvik, cache, system and data. These phones are weird.....It seems that I'm the latest in a few users to fully wipe everything including internal when flashing this and having issues. For me it was no system UI on first boot (status bar and navigation buttons). I didn't spend much time weighing alternatives, I just used LGFlashTool with the ZV4 .tot, rerooted, reflashed TWRP, then installed BarePop V2 after wiping all but internal and external. All is well now.
I can't say why this is happening but if you're thinking of wiping all the KK remnants from previous ROMs, just don't do it. I'm sure there's no harm in it being there, if "it" even exists. Although it was a good excuse to start over and update TWRP in the end, it probably isn't worth the trouble.
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